Bio-technology has substantially advanced in parallel with the use of powerful information processing systems. One such system is the BLUE GENE® Project announced in 1999. BLUE GENE is a registered trademark of International Business Machines Corporation. At that time, the BLUE GENE® Project had two high level goals: to build the world's fastest super computer and to use this unprecedented computational resource to solve the grand challenge life sciences problems such as advancing our understanding of biologically important processes, in particular, the mechanisms behind protein folding.
As a step on the way to achieving the first of these goals, the first member of the BLUE GENE® parallel computation platform (BLUE GENE) family, BLUE GENE/L®, was designed and built. In order to address the second of these goals, a research project was begun to create a classical molecular dynamics software package targeted at the Blue Gene/L architecture and to use that package for long-time and large-scale bio-molecular simulations.
Classical molecular dynamics is predominantly an n-body problem. A standard definition of an n-body problem is as follows: The n-body problem is the problem of finding, given the initial positions, masses, and velocities of n bodies, their subsequent motions as determined by classical mechanics.
An n-body problem, for example molecular dynamics (MD), proceeds as a sequence of simulation time steps. At each time step, forces on particles, in MD atoms, are computed; and then the equations of motion are integrated to update the velocities and positions of the particles. In order to compute the forces on the particles, nominally the force between each particle and every other particle is computed, a computational burden of 0(n2).
Practically speaking, molecular dynamics programs reduce the 0 (n2) by cutting off pair interactions at some distance. However for many scientifically relevant molecular systems, the computational burden due to the particle pair interactions remains large. In order to reach scientifically relevant simulation times, parallel computers are required to compute particle pair interactions rapidly. Note that the BLUE GENE/L® parallel computational platform does inter-processor communication primarily using a 3D torus network. Processor space is defined by the location of processors on the 3D torus network and communication costs between processors increase with distance.
There is a need for a system and method to enable the geometric n-body problem to be efficiently mapped (e.g., to a machine with a fundamentally geometric processor space such as BLUE GENE/L®).